Contacts of the strand formed by residues 93 - 98 (chain A) in PDB entry 5IRS
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with VAL 93 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31A MET* 4.0 26.7 - - + -
84A ARG* 3.6 4.5 - - - +
85A VAL* 2.7 53.6 + - + +
88A CYS* 3.6 33.4 - - + +
90A SER* 3.8 4.0 - - - +
91A GLY 3.7 0.6 - - - -
92A ARG* 1.3 80.5 - - - +
94A TYR* 1.3 67.1 + - - +
106A PHE* 4.4 9.0 - - + -
107A PHE 3.4 9.4 - - - +
108A TRP* 4.3 3.1 - - + -
202A DTT 4.1 10.1 - - - -
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Residues in contact with TYR 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A PHE* 3.5 26.5 - + + -
83A LYS 3.2 8.1 - - - +
84A ARG* 3.4 39.6 - - + -
85A VAL* 3.9 3.4 - - - -
91A GLY 4.4 0.7 + - - -
92A ARG* 3.6 18.4 - - - -
93A VAL* 1.3 79.4 - - - +
95A VAL* 1.3 60.5 + - - +
105A LEU 4.0 0.2 - - - +
106A PHE* 3.4 3.1 - - - -
107A PHE* 2.8 35.9 + - + +
109A MET* 3.6 36.8 - - + -
117A ASP* 3.3 17.6 + - + +
118A GLU* 2.4 28.7 + - - -
121A CYS* 3.6 29.6 - - + -
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Residues in contact with VAL 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A GLU 3.4 2.4 - - - +
82A PHE* 3.3 6.5 - - - -
83A LYS* 2.8 68.4 + - + +
85A VAL* 3.9 11.9 - - + -
94A TYR* 1.3 74.7 - - - +
96A LEU* 1.3 66.3 - - - +
97A LYS* 4.2 2.7 - - + +
104A ARG* 3.7 28.7 - - + +
105A LEU 3.3 9.0 - - - +
106A PHE* 3.5 29.4 - - + -
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Residues in contact with LEU 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A PHE* 3.8 33.7 - - + -
73A LEU* 4.6 2.0 - - + -
75A ILE* 4.8 2.5 - - + -
80A CYS* 3.9 27.6 - - + -
81A GLU 3.5 5.2 - - - +
82A PHE* 3.9 24.0 - - + -
95A VAL* 1.3 70.7 - - - +
97A LYS* 1.3 59.2 + - - +
98A PHE* 4.0 25.9 + - + -
103A LYS 4.0 0.7 - - - +
104A ARG* 3.4 4.3 - - - -
105A LEU* 2.7 48.7 + - + +
107A PHE* 4.4 4.9 - - + -
128A LEU* 3.9 19.1 - - + -
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Residues in contact with LYS 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A CYS* 3.3 3.9 - - - -
81A GLU* 2.8 45.8 + - + +
83A LYS* 4.1 26.2 - - - +
95A VAL* 3.7 4.7 - - + -
96A LEU* 1.3 73.7 - - - +
98A PHE* 1.3 81.5 + - - +
99A LYS* 3.5 15.5 + - + +
101A GLY 4.0 9.1 + - - -
102A SER* 5.5 0.6 - - - +
103A LYS 3.7 2.9 - - - +
104A ARG* 3.4 44.4 - - + +
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Residues in contact with PHE 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A LEU* 3.8 15.0 - - + -
74A ILE 5.6 0.9 - - - -
75A ILE* 3.6 20.6 - - + -
79A ASP* 3.4 15.5 - - + +
80A CYS* 3.1 30.7 - - - +
96A LEU* 4.0 19.3 - - + -
97A LYS* 1.3 78.7 + - - +
99A LYS* 1.3 65.7 + - - +
100A ALA 3.1 13.2 + - - +
101A GLY 3.0 18.2 - - - +
103A LYS* 2.9 64.8 + - + +
105A LEU* 4.9 2.7 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il